WASHINGTON — President Barack Obama’s stern words about military sexual assault have stirred up trouble in court, raising anew the specter of higher-ups unfairly steering the outcome of criminal cases.

Now, appellate judges have stopped a Navy court-martial in order to figure out, in part, whether the commander in chief’s rhetoric went too far. What happens next could further shape a military justice system that’s being pressed hard by politicians and uniformed leaders of all stripes.

Already, one Navy judge in Hawaii has determined that Obama’s tough talk amounted to at least the appearance of unlawful command influence. As a result, the judge took away prosecutors’ ability to force punitive discharges on two separate defendants.

This week, responding to the government’s urgent request, the U.S. Navy-Marine Corps Court of Criminal Appeals agreed to stop one of the Hawaiian cases while it tries to sort out the problem.

“The military trial judge’s ruling in those cases is potentially very important,” defense attorney Richard Stevens said Thursday. “It gives voice to complaints and motions the defense community has been filing in military sexual assault cases regarding unlawful command influence by not only the president, but the secretary of defense, service secretaries, service branch chiefs of staff and others.”

Obama stepped into the controversy on May 7.

“The bottom line is, I have no tolerance for this. I expect consequences,” he said. “If we find out somebody’s engaging in this stuff, they’ve got to be held accountable, prosecuted, stripped of their positions, court-martialed, fired, dishonorably discharged. Period.”

In its order Monday, the Navy-Marine appeals court stopped a court-martial scheduled to start the same day at Pearl Harbor. The Washington Navy Yard-based appellate court eventually could rule just on the paperwork or could order oral arguments. Eventually, the case appears bound for the U.S. Court of Appeals for the Armed Forces, where judges already confront tricky unlawful command influence questions.

“Ultimately, the prohibition on command influence is about constitutional rights, and whether military justice proceedings can provide service members with due process of law when the leaders who control the process are demanding certain results,” said Marine Corps Reserve Maj. Babu Kaza.

He is currently awaiting an appeals court decision on a separate unlawful command influence case. The military justice system is particularly sensitive to command influence, because of the obedience and top-down discipline that's part of the military culture.

Among the trickiest questions is whether unlawful command influence complaints can even be applied to civilians, like the secretary of the Navy or the president. While the president is atop the chain of command, he is not subject to the Uniform Code of Military Justice

For Navy enlisted men Ernest J. Johnson and Javier Fuentes Jr., who are accused of sexual assault in two separate incidents, what happens next will follow them for the rest of their lives. If the appellate court overturns the trial judge and the sailors are ultimately convicted and sentenced to punitive discharges, among other penalties, they will carry a permanent legal stigma and loss of benefits.

More broadly, the appellate judges could be determining whether the political inveighing against military sexual assault will have the unintended consequence of making prosecutions and punishment more difficult.

In recent months, Obama and top Pentagon officials, both uniformed and civilian, have persistently demanded tougher punishments for those convicted of sexual assault.

“Such statements do tend to show the court and the public that the actions of (officers) in individual courts-martial cannot be counted on to escape the notice and scrutiny of leadership,” Navy Cmdr. Marcus N. Fulton, a military judge, noted in one of two related rulings last week.

The Pentagon reports that 3,374 sexual assaults on active-duty members of the military were alleged in 2012. Extrapolating from a small survey, the Pentagon also estimates that upward of 26,000 sexual assaults may take place annually. Several specific episodes have heightened political attention, including an Air Force general overturning the sexual assault conviction of a fellow fighter pilot.

Johnson, a ship’s serviceman second class, is charged with sexually assaulting another sailor who was asleep or intoxicated. Fuentes, a seaman, was also charged with sexual assault in a separate case. In asking the judge for relief, defense attorneys cited Obama’s statements and those of lawmakers, like Democratic Sen. Claire McCaskill of Missouri, who blocked the promotion of a female Air Force general who had overturned a sexual assault conviction.

In similar 14-page rulings issued early last week in both cases, Fulton concluded that certain “senior civilians,” including the president – though not senators – may be covered under the rules against unlawful command influence. In particular, Fulton cited Obama’s demand for dishonorable discharges.

“It is reasonable to suppose that a commander would view the president’s statement about dishonorable discharges as sending the word down . . . as to a desired result in a criminal case which will please the leadership of our armed forces,” Fulton wrote.

In response, Ervasti wrote for the government that Obama’s statements simply “assured these people that he takes sexual assaults very seriously” and that the president’s words should not be interpreted to “grant a windfall to every sexual assault perpetrator in the foreseeable future.”

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